PhoneGap Build does not enforce much structure beyond having a "config.xml" file, and that it either needs to be a sibling of "index.html" or in the parent directory with "index.html" inside a "www" folder. Beyond that, you can use whatever structure you want.

Valid structures:

zip-root/

config.xml

index.html

res/

etc.

zip-root/

config.xml

res/

www/

index.html

etc.

(Note: access to icons and splash resources are relative to config.xml, and usually placed in a res/ directory that's a sibling to config.xml.)